If you're seating bullets in bottleneck cases that headpace on their shoulder, note they all have a small spread in thousandths in their head to shoulder dimension. That gets transferred to the bullet in the chamber throat.
While you may have seated all the bullets to .0001" tolerance in seater plug contact point to case head, if there's a .004" spread in case head to shoulder measurement, that's the spread (+/- .0001") your bullet will be in the chamber neck. If you had tried to get a .005" bullet jump to the lands, its now got that much spread.
This is why I soft-seat bullets about .010" long for the chamber to ensure they're all set back just right and touching the lands very consistantly. But I size the fired case necks just enough to grip the bullet firmly enough so a chambered round can be ejected and take the bullet with it. Three cheers for dies with different neck diameters for different case neck wall thicknesses.
If you want accurate bullet seating measurements, make them relative to the case shoulder at some reference diameter.